TB-Profiler result

Run: SRR11972182
Summary

Run ID: SRR11972182

Sample name:

Date: 03-04-2023 05:31:11

Number of reads: 142211

Percentage reads mapped: 87.5

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
rpoB 761149 p.Arg448Gln missense_variant 0.33 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288795 c.446dupA frameshift_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5521 c.282G>A synonymous_variant 0.29
gyrB 7160 p.Ala641Thr missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576446 p.Thr367Ala missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760315 p.Val170Ala missense_variant 1.0
rpoB 761657 c.1851C>A synonymous_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766057 c.2688C>A synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407511 c.-171T>C upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.4
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.13
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.15
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.17
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.15
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.15
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.15
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.15
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.15
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.15
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.22
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.25
rrl 1474718 n.1061A>G non_coding_transcript_exon_variant 0.17
rrl 1475433 n.1776A>G non_coding_transcript_exon_variant 0.22
rrl 1475870 n.2213G>A non_coding_transcript_exon_variant 0.15
rrl 1475967 n.2310C>T non_coding_transcript_exon_variant 0.2
inhA 1674914 p.Val238Asp missense_variant 0.33
rpsA 1834096 c.555G>T synonymous_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170592 c.21G>T synonymous_variant 0.11
Rv1979c 2222290 c.874delG frameshift_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448388 c.-116C>A upstream_gene_variant 0.17
Rv3083 3448773 c.270G>T synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840748 p.Gln225* stop_gained 0.18
alr 3841255 p.Ala56Thr missense_variant 0.22
alr 3841546 c.-126C>A upstream_gene_variant 0.14
clpC1 4040382 p.Ile108Thr missense_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241716 c.1854C>T synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243932 p.Arg234Cys missense_variant 0.29
embB 4245794 c.-720G>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338663 c.-142G>A upstream_gene_variant 0.25
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407958 p.Ala82Val missense_variant 0.29